•For docks, what type of decking will be used? If grated, provide manufacturer's name/

address/grating type, and percent light transmittance (%LT) of the grating design used? 

If wooden planks, what is the proposed spacing between the deckboards (1⁄2-inch, 3⁄4-inch, 

1-inch, other?). Has the applicant been advised that COE-NMFS project review is 

significantly simplified and expedited for dock designs incorporating >43% LT grated 

decking, or 1-inch deckboard- and walkway-spacing, over Johnson's seagrass areas? 

Proposed height of dock? Orientation of the dock (N, S, etc.)?

•Piling construction methodology. Are pile driving methods adequately described and are 

potential impacts to species adequately addressed? Will submerged aquatic vegetation 

(SAV) be impacted by pile installation? If necessary, will the applicant's contractor 

adjust the spacing between piles to avoid driving piles onto Johnson's seagrass? Avoiding 

all piling impacts to JSG will significantly simplify and expedite the COE-NMFS project 

review process.

•Number of new slips and size of slips, if applicable. If new construction includes Highand-Dry boat storage, what is the High-and-Dry vessel storage capacity?

•How big are the boats that are planned to be moored at the dock (either in the water or on a 

boatlift), if known? 

•For all projects not involving docks or marinas (i.e., seawalls, jetties, etc.), please provide 

project description.

•Dredging? If yes, describe depth of cut, dredge type used, how many cubic yards, and 

what will be done with the spoil. Describe bottom sediments. Describe area 

hydrodynamics, i.e., average current speed and direction.

N/A

N/A

N/A

N/A

N/A

Piles will be driven to load bearing capacity for E80 live loads. Piles will be driven with a steel pile 

driving template placed to prevent movement of the pile group. SAV were not observed within the 

project footprint.
•Blasting? If yes, describe explosive weights, blasting plan, etc.

•What is the intended construction schedule (how many days, weeks, or months for inwater work)?

Potential Effects on Species/Critical Habitat:

•Please explain any impacts/effects to the critical habitat's primary constituent elements -

PCEs)? Please identify which critical habitat unit(s) is being affected (e.g., Gulf sturgeon 

have 14 units, seven under NMFS jurisdiction and seven under FWS jurisdiction).

•What will the effects be, if any, to each PCE?

•Square footage to be affected by project?

•Will mangroves be impacted? Explain and quantify impacts.

•How will the habitat be changed/altered as a result of the action? Could or will the 

alteration affect listed species? How?

N/A

N/A

N/A

Work will be completed by December 2016

18,615 sq ft will be affected by the project footprint.

No mangroves were present within the Assessment Area

Approximately 18,615 sq. ft. of surface waters will be impacted by the installation of riprap and pilings, 

and shading of non-vegetated surface water by the new bridge. The proposed bridge construction 

may have direct short-term adverse effects on the water quality in the project vicinity. Effects to the 

managed species known to occur in the project vicinity would include installation of the pilings and 

shade resulting from bridge deck construction. Pilings would ultimately result in a beneficial effect to 

species/life stages that prefer such structures as habitat, such as adult goliath grouper, gray snapper, 

and mutton snapper. Lifecycle functions will not be affected by the proposed activities.





•For docks, what type of decking will be used? If grated, provide manufacturer's name/

address/grating type, and percent light transmittance (%LT) of the grating design used? 

If wooden planks, what is the proposed spacing between the deckboards (1⁄2-inch, 3⁄4-inch, 

1-inch, other?). Has the applicant been advised that COE-NMFS project review is 

significantly simplified and expedited for dock designs incorporating >43% LT grated 

decking, or 1-inch deckboard- and walkway-spacing, over Johnson's seagrass areas? 

Proposed height of dock? Orientation of the dock (N, S, etc.)?

•Piling construction methodology. Are pile driving methods adequately described and are 

potential impacts to species adequately addressed? Will submerged aquatic vegetation 

(SAV) be impacted by pile installation? If necessary, will the applicant's contractor 

adjust the spacing between piles to avoid driving piles onto Johnson's seagrass? Avoiding 

all piling impacts to JSG will significantly simplify and expedite the COE-NMFS project 

review process.

•Number of new slips and size of slips, if applicable. If new construction includes Highand-Dry boat storage, what is the High-and-Dry vessel storage capacity?

•How big are the boats that are planned to be moored at the dock (either in the water or on a 

boatlift), if known? 

•For all projects not involving docks or marinas (i.e., seawalls, jetties, etc.), please provide 

project description.

•Dredging? If yes, describe depth of cut, dredge type used, how many cubic yards, and 

what will be done with the spoil. Describe bottom sediments. Describe area 

hydrodynamics, i.e., average current speed and direction.

N/A

N/A

N/A

N/A

N/A

Piles will be driven to load bearing capacity for E80 live loads. Piles will be driven with a steel pile 

driving template placed to prevent movement of the pile group. SAV were not observed within the 

project footprint.
•Blasting? If yes, describe explosive weights, blasting plan, etc.

•What is the intended construction schedule (how many days, weeks, or months for inwater work)?

Potential Effects on Species/Critical Habitat:

•Please explain any impacts/effects to the critical habitat's primary constituent elements -

PCEs)? Please identify which critical habitat unit(s) is being affected (e.g., Gulf sturgeon 

have 14 units, seven under NMFS jurisdiction and seven under FWS jurisdiction).

•What will the effects be, if any, to each PCE?

•Square footage to be affected by project?

•Will mangroves be impacted? Explain and quantify impacts.

•How will the habitat be changed/altered as a result of the action? Could or will the 

alteration affect listed species? How?

N/A

N/A

N/A

Work will be completed by December 2016

3,936 sq ft will be affected by the project footprint.

No mangrove were present within the Assessment Area.

Approximately 3,936 sq. ft. of surface waters and wetlands will be impacted by the installation of riprap

 and pilings, and shading of non-vegetated surface water by the new bridge. The proposed bridge 

construction may have direct short-term adverse effects on the water quality in the project vicinity. 

Effects to the managed species known to occur in the project vicinity would include installation of the t 

pilings and shade resulting from bridge deck construction. Pilings would ultimately result in a beneficial 

effect to species/life stages that prefer such structures as habitat, such as adult goliath grouper, gray 

snapper, and mutton snapper. Lifecycle functions will not be affected by the proposed activities.





•For docks, what type of decking will be used? If grated, provide manufacturer's name/

address/grating type, and percent light transmittance (%LT) of the grating design used? 

If wooden planks, what is the proposed spacing between the deckboards (1⁄2-inch, 3⁄4-inch, 

1-inch, other?). Has the applicant been advised that COE-NMFS project review is 

significantly simplified and expedited for dock designs incorporating >43% LT grated 

decking, or 1-inch deckboard- and walkway-spacing, over Johnson's seagrass areas? 

Proposed height of dock? Orientation of the dock (N, S, etc.)?

•Piling construction methodology. Are pile driving methods adequately described and are 

potential impacts to species adequately addressed? Will submerged aquatic vegetation 

(SAV) be impacted by pile installation? If necessary, will the applicant's contractor 

adjust the spacing between piles to avoid driving piles onto Johnson's seagrass? Avoiding 

all piling impacts to JSG will significantly simplify and expedite the COE-NMFS project 

review process.

•Number of new slips and size of slips, if applicable. If new construction includes Highand-Dry boat storage, what is the High-and-Dry vessel storage capacity?

•How big are the boats that are planned to be moored at the dock (either in the water or on a 

boatlift), if known? 

•For all projects not involving docks or marinas (i.e., seawalls, jetties, etc.), please provide 

project description.

•Dredging? If yes, describe depth of cut, dredge type used, how many cubic yards, and 

what will be done with the spoil. Describe bottom sediments. Describe area 

hydrodynamics, i.e., average current speed and direction.

N/A

N/A

N/A

N/A

N/A

Piles will be driven to load bearing capacity for E80 live loads. Piles will be driven with a steel pile 

driving template placed to prevent movement of the pile group. SAV were not observed within the 

project footprint.
•Blasting? If yes, describe explosive weights, blasting plan, etc.

•What is the intended construction schedule (how many days, weeks, or months for inwater work)?

Potential Effects on Species/Critical Habitat:

•Please explain any impacts/effects to the critical habitat's primary constituent elements -

PCEs)? Please identify which critical habitat unit(s) is being affected (e.g., Gulf sturgeon 

have 14 units, seven under NMFS jurisdiction and seven under FWS jurisdiction).

•What will the effects be, if any, to each PCE?

•Square footage to be affected by project?

•Will mangroves be impacted? Explain and quantify impacts.

•How will the habitat be changed/altered as a result of the action? Could or will the 

alteration affect listed species? How?

N/A

N/A

N/A

Work will be completed by December 2016

37,350 sq ft will be affected by the project footprint.

Mangrove impacts are not anticipated. 

Approximately 37,350 sq. ft. of surface waters and wetlands will be impacted by the installation of 

riprap and pilings, and shading of non-vegetated surface water by the new bridge. The proposed 

bridge construction may have direct short-term adverse effects on the water quality in the project 

vicinity. Effects to the managed species known to occur in the project vicinity would include installation

 of the replacement pilings and shade resulting from bridge deck construction. Pilings would ultimately 

result in a beneficial effect to species/life stages that prefer such structures as habitat, such as adult 

goliath grouper, gray snapper, and mutton snapper. Lifecycle functions will not be affected by the 

proposed activities.





•For docks, what type of decking will be used? If grated, provide manufacturer's name/

address/grating type, and percent light transmittance (%LT) of the grating design used? 

If wooden planks, what is the proposed spacing between the deckboards (1⁄2-inch, 3⁄4-inch, 

1-inch, other?). Has the applicant been advised that COE-NMFS project review is 

significantly simplified and expedited for dock designs incorporating >43% LT grated 

decking, or 1-inch deckboard- and walkway-spacing, over Johnson's seagrass areas? 

Proposed height of dock? Orientation of the dock (N, S, etc.)?

•Piling construction methodology. Are pile driving methods adequately described and are 

potential impacts to species adequately addressed? Will submerged aquatic vegetation 

(SAV) be impacted by pile installation? If necessary, will the applicant's contractor 

adjust the spacing between piles to avoid driving piles onto Johnson's seagrass? Avoiding 

all piling impacts to JSG will significantly simplify and expedite the COE-NMFS project 

review process.

•Number of new slips and size of slips, if applicable. If new construction includes Highand-Dry boat storage, what is the High-and-Dry vessel storage capacity?

•How big are the boats that are planned to be moored at the dock (either in the water or on a 

boatlift), if known? 

•For all projects not involving docks or marinas (i.e., seawalls, jetties, etc.), please provide 

project description.

•Dredging? If yes, describe depth of cut, dredge type used, how many cubic yards, and 

what will be done with the spoil. Describe bottom sediments. Describe area 

hydrodynamics, i.e., average current speed and direction.

N/A

N/A

N/A

N/A

N/A

If pile installation is necessary, piles will be driven to load bearing capacity for E80 live loads. 

Piles will be driven with a steel pile driving template placed to prevent movement of the pile 

group. SAV were not observed within the project footprint.
•Blasting? If yes, describe explosive weights, blasting plan, etc.

•What is the intended construction schedule (how many days, weeks, or months for inwater work)?

Potential Effects on Species/Critical Habitat:

•Please explain any impacts/effects to the critical habitat's primary constituent elements -

PCEs)? Please identify which critical habitat unit(s) is being affected (e.g., Gulf sturgeon 

have 14 units, seven under NMFS jurisdiction and seven under FWS jurisdiction).

•What will the effects be, if any, to each PCE?

•Square footage to be affected by project?

•Will mangroves be impacted? Explain and quantify impacts.

•How will the habitat be changed/altered as a result of the action? Could or will the 

alteration affect listed species? How?

N/A

N/A

N/A

Work will be completed by December 2016

Mangrove impacts are not anticipated. 

Currently the proposed project will not result in modification to any habitats; however, if in-water 

work is deemed necessary, surface waters and wetlands may be impacted through installation of 

riprap and pilings, as well as shading of non-vegetated surface waters. If in-water work is deemed 

necessary, there may be direct short-term adverse effects on the water quality in the project 

vicinity. Effects to the managed species known to occur in the project vicinity may include 

installation of pilings (temporary or permanent) and shade resulting from additional bridge deck 

construction. Pilings would ultimately result in a beneficial effect to species/life stages that prefer 

such structures as habitat, such as adult goliath grouper, gray snapper, and mutton snapper. 

Lifecycle functions will not be affected by the proposed activities.

The proposed work is limited to updates to the existing structures. If in-water work is necessary, the

maximum footprint would be 14,381 square feet (footprint of bridge)





•For docks, what type of decking will be used? If grated, provide manufacturer's name/

address/grating type, and percent light transmittance (%LT) of the grating design used? 

If wooden planks, what is the proposed spacing between the deckboards (1⁄2-inch, 3⁄4-inch, 

1-inch, other?). Has the applicant been advised that COE-NMFS project review is 

significantly simplified and expedited for dock designs incorporating >43% LT grated 

decking, or 1-inch deckboard- and walkway-spacing, over Johnson's seagrass areas? 

Proposed height of dock? Orientation of the dock (N, S, etc.)?

•Piling construction methodology. Are pile driving methods adequately described and are 

potential impacts to species adequately addressed? Will submerged aquatic vegetation 

(SAV) be impacted by pile installation? If necessary, will the applicant's contractor 

adjust the spacing between piles to avoid driving piles onto Johnson's seagrass? Avoiding 

all piling impacts to JSG will significantly simplify and expedite the COE-NMFS project 

review process.

•Number of new slips and size of slips, if applicable. If new construction includes Highand-Dry boat storage, what is the High-and-Dry vessel storage capacity?

•How big are the boats that are planned to be moored at the dock (either in the water or on a 

boatlift), if known? 

•For all projects not involving docks or marinas (i.e., seawalls, jetties, etc.), please provide 

project description.

•Dredging? If yes, describe depth of cut, dredge type used, how many cubic yards, and 

what will be done with the spoil. Describe bottom sediments. Describe area 

hydrodynamics, i.e., average current speed and direction.

N/A

N/A

N/A

N/A

N/A

If pile installation is necessary, piles will be driven to load bearing capacity for E80 live loads. Piles

 will be driven with a steel pile driving template placed to prevent movement of the pile 

group. SAV were not observed within the project footprint.
•Blasting? If yes, describe explosive weights, blasting plan, etc.

•What is the intended construction schedule (how many days, weeks, or months for inwater work)?

Potential Effects on Species/Critical Habitat:

•Please explain any impacts/effects to the critical habitat's primary constituent elements -

PCEs)? Please identify which critical habitat unit(s) is being affected (e.g., Gulf sturgeon 

have 14 units, seven under NMFS jurisdiction and seven under FWS jurisdiction).

•What will the effects be, if any, to each PCE?

•Square footage to be affected by project?

•Will mangroves be impacted? Explain and quantify impacts.

•How will the habitat be changed/altered as a result of the action? Could or will the 

alteration affect listed species? How?

N/A

N/A

N/A

Work will be completed by December 2016

The proposed work is limited to updates to the existing structures, with no new footprint. If 

in-water work is necessary, the maximum footprint would be 13,825 square ft (footprint of bridge)

Mangrove impacts are not anticipated. Potential trimming will be done in accordance with 

FDEP Guidance. 

Currently the proposed project will not result in modification to any habitats; however, if in-water 

work is deemed necessary, surface waters and wetlands may be impacted through installation of 

riprap and pilings, as well as shading of non-vegetated surface waters. If in-water work is deemed 

necessary, there may be direct short-term adverse effects on the water quality in the 

project vicinity. Effects to the managed species known to occur in the project vicinity may 

include installation of pilings (temporary or permanent) and shade resulting from additional 

bridge deck construction. Pilings would ultimately result in a beneficial effect to species/life stages 

that prefer such structures as habitat, such as adult goliath grouper, gray snapper, and mutton 

snapper. Lifecycle functions will not be affected by the proposed activities. 



Correspondence:

AMEC 

404 SW 140th Terrace 

Newberry, Florida 

USA 32669-3000 

Tel + 1 352 332 3318 

Fax + 1 352 333 6622 amec.com 

 

Page 1 of 9

January 24, 2014 

Mr. Andrew Philips 

United States Army Corps of Engineers 

Cocoa Permits Section 

400 High Point Drive, Suite 600 

Cocoa, Florida, 32926 

Subject: Addendum 1 to AAF NOAA Fisheries Biological Assessment dated 

September 1, 2013 

Dear Mr. Phillips: 

AMEC Environment & Infrastructure, Inc. (AMEC), on behalf of All Aboard Florida – Operations LLC 

(AAF), submitted the Biological Assessment for the All Aboard Florida Passenger Rail Project from 

Orlando to Miami, Florida: Species under NOAA Fisheries Jurisdiction to the United States Army 

Corps of Engineers (USACE) on September 3, 2013 (BA). Following submission of this document, 

further study was conducted by representatives of AAF that examined the capability of existing 

bridges and 6 bridges were identified as requiring additional assessment. The results of the 

additional assessment concluded that each of the four (4) railroad bridges crossing the Eau Gallie 

River, Crane Creek, Turkey Creek, and the Sebastian River would eventually require replacement 

while the bridges crossing the Loxahatchee River and St. Lucie River would eventually require more 

substantial refurbishment than initially proposed. The locations of the aforementioned bridges are 

illustrated on Figure 1 (Attachment 1). 

In light of the foregoing, AAF is studying whether to complete the Project with additional work at 

these locations as part of the initial construction of the Project (the “Bridge Alternative”). The Bridge 

Alternative includes the proposal to (a) complete new bridges alongside existing structures at the 

following locations due to the potential for those existing railroad bridges crossings to be eligible for 

listing on the National Register of Historic Places (NRHP): the Eau Gallie River, Crane Creek, 

Turkey Creek, and the Sebastian River; and (b) complete additional work at the bridges crossing the 

Loxahatchee River and St. Lucie River. The following summary details the proposed activities at 

each crossing that are being contemplated as part of the Bridge Alternative: 

1. Mile Post (MP) 282.50 (Loxahatchee River) – Rehabilitation or replacement of existing structural 

steel girders, concrete piers, and mechanical and electrical systems. The process will return the 

span back to a movable double track bridge. 

2. MP 260.93 (St. Lucie River) – Rehabilitation of existing structural steel, concrete piers, and 

mechanical and electrical systems. 

3. MP 212.07 (Sebastian River) - Construction of twin new independent ballast deck structures 

located to the east of the existing railroad bridge. The ballast deck structures will be supported 

by concrete piers. 

4. MP 197.70 (Turkey Creek) – Construction of new twin 181-ft independent ballast deck structures 

located on the west side of the existing bridge. The ballast deck structures will be supported by 

concrete piers. 
Addendum 2 to AAF NOAA Biological Assessment dated September 3, 2013 

AMEC Project No.: 6063120212 January 2014 

Page 2 of 9 

5. MP 194.36 (Crane Creek) – Construction of one new 650-ft independent ballast deck structure 

located on the east sides of the existing railroad bridge and one new single track bridge in the 

footprint of the removed western bridge. The new structures will be supported by concrete piers. 

6. MP 190.47 (Eau Gallie River) - Construction of twin new 575-ft independent ballast deck 

structures located to the east of the existing railroad bridge. The ballast deck will be supported 

by concrete piers. 

Although in-water work is currently not proposed at the Loxahatchee River and St. Lucie River, there 

may be a potential need for in-water work, pending further examination of the existing bridge 

structures, and required construction methods; therefore, ESA consultation should be conducted 

assuming in-water work at these locations. In addition, The existing historic bridges at the Eau Gallie 

River, Crane Creek, Turkey Creek, and Sebastian RIver will be left in place and maintained by FEC. 

FEC will be responsible for ensuring that overtime the deterioration of the bridges does not result in 

impacts to navigation, floodplains, wetlands, or ecological habitat through removal and relocation 

prior to deterioration and/or removal of fallen debris. 

In addition, silt fence and floating turbidity barriers will be installed and maintained during 

construction in accordance with performance standards for erosion and sediment control and 

stormwater treatment set forth in section 62-40.432, FAC. 

In light of the possibility that the Bridge Alternative may be incorporated into the Proposed Project 

(as defined in the BA), this addendum has been prepared to provide information regarding these 

additional bridge assessment areas (Bridge Assessment Areas) and potential impacts to protected 

species associated with the Bridge Alternative. 

1.0 Existing Conditions and Action Area 

The route for the Proposed Project is approximately 235 miles long. The North South Corridor lies 

along the Atlantic coast from Miami to Cocoa. The six bridges affected by the Bridge Alternative 

include bridges at Eau Gallie River, Crane Creek, Turkey Creek, Sebastian River, St., Lucie River, 

and Loxahatchee River (Attachment 1-Figure 1). 

1.1 Survey Methods 

Desktop surveys for known distribution of federally protected species were performed. County 

records on listed species available from the USFWS1 and the Florida Natural Area Inventory (FNAI) 

Biodiversity Matrix2

 provided information on federally protected species documented, or expected to 

occur in the vicinity of the Project Area. 

Field surveys included wetland delineations, pedestrian transects within Project Areas, incidental 

observations of protected species’ presence and habitat type and quality; in-water seagrass and 

benthic resource surveys; and qualitative evaluation of habitats in the vicinity of proposed 

construction sites. 

 

1

 United States Fish and Wildlife Service (USFWS). 2012. Species by County Report. Website: http://ecos.fws. gov/tess_public/. 

Accessed August 2012. 

2

 Florida Natural Area Inventory (FNAI). 2013. Biodiversity Matrix. Website accessed: http://www.fnai.org/biointro.cfm 
Addendum 2 to AAF NOAA Biological Assessment dated September 3, 2013 

AMEC Project No.: 6063120212 January 2014 

Page 3 of 9 

In October 2013, AMEC scientists evaluated the six Bridge Assessment Areas that are slated for 

improvements on account of the Bridge Alternative that may require in-water work. In-water benthic 

surveys were completed at all locations where there was potential for seagrass to occur. AMEC 

performed visual in-water reconnaissance of the Bridge Assessment Areas. The purpose of the 

benthic surveys was to characterize the bottom composition as well as determine the presence of 

seagrass beds, oyster beds, sponges, red mangrove wetlands, and other benthic resources. Visual 

assessment from bridge decks was used to identify whether or not an in-water survey should be 

conducted. Where deemed appropriate, benthic surveys were performed in accordance with NOAA 

Fisheries guidance for assessing medium and large project3. As part of the in-water seagrass survey 

protocol, if seagrasses were determined to be rooted within the assessment area, field personnel would 

delineate and quantify patch distribution4. 

1.2 Survey Results 

The desktop survey identified the following federally listed plants and animals under NOAA Fisheries 

jurisdiction that might be found in the Project Area: sea turtles- Loggerhead (Caretta caretta), Green 

(Chelonia mydas), Kemp’s Ridley (Lepidochelys kempii), Hawksbill (Eremochelys imbricate), and 

Leatherback (Demochelys coriacea); smalltooth sawfish (Pristis pectinata), and Johnson’s seagrass 

(Halophila johnsonii). These species are discussed in detail in the BA. Critical habitat for these 

species was not identified within the vicinity of the Bridge Assessment Areas. 

Potential habitat for sea turtles and smalltooth sawfish were observed during the field studies, 

including mangrove wetlands. No populations of Johnson’s seagrass were identified within the 

Bridge Assessment Areas and none of the above referenced species were observed during the field 

surveys. 

The results of the field surveys including the benthic resource surveys at each Bridge Assessment 

Area are described below and summarized in Table 1. The design for the bridges is not final yet; 

however, direct wetland impacts have been estimated based on the proposed footprint of the bridge, 

as the maximum potential impact acreage (including shading). Estimated wetland and surface water 

impacts at the six Bridge Assessment Areas are outlined in Table 2. A photograph log for the bridge 

project areas is located in Attachment 2. Aerial photographs of each bridge location are located in 

Attachment 3. 

Eau Gallie River 

Wetlands along the Eau Gallie River are limited to a narrow fringe along the shorelines. The steep 

river banks along the Eau Gallie River near the FEC bridge as well as the placement of ballast 

between the abutments and the river reduce the amount of area that wetland resources can 

establish. Due to the aforementioned disturbance, the vegetation within the fringe wetland and 

associated upland is comprised of mainly Florida Exotic Pest Plant Council (FLEPPC) listed invasive 

species (i.e. Brazilian Pepper (Schinus terebinthifolius) and Australian Pine (Casuarina spp.). 

Although the wetland has been diminished and is currently dominated by invasive vegetation, the 

tidally influenced brackish water has allowed for the establishment of a few white mangroves 

 

3

 National Oceanic Atmospheric Association (NOAA) National Marine Fisheries Service. 2012. Recommendations for Sampling 

Halophila johnsoii at a Project Site. Website. http://sero.nmfs.noaa.gov/pr/docs/JSG%20 Survey%20Guidelines.pdf Accessed 

August 2012 

4

 Florida Fish and Wildlife Conservation Commission (FWC) 2011. Recommended Survey Protocols for Estuarine and Marine 

Submerged Aquatic Vegetation (SAV) related to Permitting Applications (Draft). 
Addendum 2 to AAF NOAA Biological Assessment dated September 3, 2013 

AMEC Project No.: 6063120212 January 2014 

Page 4 of 9 

(Laguncularia racemosa) along the northern bank of the Eau Gallie River. Their presence just west 

of the bridge platform along the northern bank is a positive characteristic when compared to the 

surrounding ecosystem. Additional plants observed growing within the Bridge Assessment Area 

included spike rush (Eleocharis spp), coastal willow (Salix caroliniana), and saw palmetto (Sabal 

palmetto). Although visibility was noted as being moderate, AMEC scientists were able to view the 

bottom without obstruction. The results of the benthic survey indicated that the Eau Gallie River 

bottom in the Bridge Assessment Area was comprised of a slurry of mud, small rocks (less than 1 

inch in size) and crushed shells. The survey did identify a few oyster shells within the Bridge 

Assessment Area; however, no oyster beds were observed. Given the composition of the 

aforementioned substrate and water quality, the aquatic environment near where the FEC railroad 

bridge does not appear to be conducive to either seagrass or oyster bed establishment. AMEC did 

not observe the presence of seagrasses or other submerged aquatic vegetation (SAV), oyster beds, 

sponges or associated species within the Bridge Assessment Area. 

Crane Creek 

Vegetation along the slopes of Crane Creek bridge included: common reed (Phragmites australis), 

pennywort (Hydrocotyle spp), and maidencane (Panicum hem.). The list of species growing within 

the delineated wetland also included Brazilian Pepper and Lead Tree (Leucaena leucocephala). 

Each of the aforementioned species is listed as a Category I FLEPPC invasive plant. Although, the 

bridge is located in a tidally influenced portion of Crane Creek, the observed wetland vegetation is 

indicative of freshwater wetland systems. During the October 9, 2013 survey, field personnel noted 

that mangroves were not observed within or near the above referenced Bridge Assessment Area. 

Additional signs of disturbance within the wetland included the placement of ballast at the approach 

to the abutment on the south side of the bridge. The results of the benthic survey indicated that 

Crane Creek bottom of the Bridge Assessment Area was comprised of small rocks (less than 0.5 

inches in diameter), crushed shells, and highly decomposed organic matter. Based on the observed 

conditions, the aquatic environment near the Crane Creek railroad bridge does not appear to be 

conducive to either seagrass or oyster bed establishment. AMEC did not observe the presence of 

seagrasses or other submerged aquatic vegetation, oyster beds, sponges or associated species 

within the Bridge Assessment Area. 

Turkey Creek 

Due to the relatively steep slopes along Turkey Creek in the Bridge Assessment Area, wetlands are 

limited to a fringe wetland surrounding the bridge. Immediately to the west of the Bridge 

Assessment Areas, Turkey Creek meanders through a large stand of cattails (Typha lancifolia). 

Additional vegetation observed near the Bridge Assessment Area included cabbage palms (Sabal 

palmetto), Brazilian Pepper, and air potato (Dioscorea bulbifera). Both Brazilian Pepper and air 

potato are listed as a Category I FLEPPC invasive species. Although it is assumed that due to the 

Bridge Assessment Areas close proximity to the inter-coastal waterway (ICW), the water within the 

creek would be brackish; the observed lack of halophytic vegetation indicates the water within 

Turkey Creek is primarily fresh. Due to extremely poor visibility (black tinted water) and the 

presence of a large American Alligator, the survey only included a small area near the south and 

north banks of Turkey Creek near the railroad bridge. The limited benthic survey indicated that the 

bottom is mainly comprised of small rocks and muck. Based on the field observations of the 

substrate, the presence of freshwater vegetation, and black tinted water, the Turkey Creek Bridge 

Assessment Area does not appear to provide suitable habitat for seagrass or oysters beds. AMEC 

did not observe the presence of seagrasses or other submerged aquatic SAV, oysters, sponges or 

associated species within the Bridge Assessment Area. 
Addendum 2 to AAF NOAA Biological Assessment dated September 3, 2013 

AMEC Project No.: 6063120212 January 2014 

Page 5 of 9 

Sebastian River 

The steep river banks along the Sebastian River near the bridge as well as the placement of ballast 

between the abutments and the river have reduced the amount of wetland resources within the 

Bridge Assessment Area. Due to the steep banks and presence of ballast, the wetland area in the 

Bridge Assessment Area is limited to a narrow fringe along the river shoreline. Due to the 

aforementioned disturbance, the vegetation within the fringe wetland and associated upland was 

comprised of mainly of FLEPPC listed invasive species (i.e. Brazilian Pepper and air potato). There 

were no mangroves growing within the Bridge Assessment Area. Historically, the Sebastian River 

served as habitat for protected seagrasses and large oyster beds; however, residents and fisherman 

have stated that the aforementioned resources have become either non-existent in the case of 

seagrasses or in the case of the oysters contaminated and diminished. Although visibility was noted 

as being moderate and the water maintained a substantial chop, AMEC scientists were able to view 

the bottom without obstruction. The results of the benthic survey indicated that the shallow 

Sebastian River bottom of the Bridge Assessment Area was comprised of unconsolidated small 

rocks (less than 0.5 inch in size), highly decomposed organic matter, and shells. Although a very 

shallow sand bar was noted as being present near the middle of the river, seagrasses were not 

observed growing within or adjacent to the Bridge Assessment Area. The survey did identify an 

oyster bed on the northwest side of the bridge; however, it was mainly comprised of broken shells. 

Although portions of the Bridge Assessment Area maintained suitable substrate, the current aquatic 

environment does not appear to be conducive to seagrass establishment. AMEC did not observe 

the presence of seagrasses or other SAV, sponges or associated species within the Bridge 

Assessment Area. 

St. Lucie River 

The armoring of the shoreline with concrete bulkheads and metal sheet piling associated with the 

existing rail bridge has resulted in limited wetland resources within the Bridge Assessment Area. 

During the October 7, 2013 survey, a few red mangroves (Rhizophora mangle) and white 

mangroves were observed growing on both the north and south banks of the St. Lucie River near the 

Bridge Assessment Area. The red mangroves on the north side of the river were noted as being 

more mature than those on the south side of the river. Additional species observed growing within 

the fringe wetland included sea grape (Coccoloba uvifera) and Brazilian Pepper. AMEC scientists 

noted that visibility within the river was extremely poor with substantial amounts of sediment 

suspended in the water column. During the survey AMEC scientists noted that a thick layer of 

sediment covered the bottom of the river throughout most of the Bridge Assessment Area. Based on 

the observed turbid water and thick sediment layer covering the river bottom, the aquatic 

environment currently does not appear to be conducive to seagrass or oyster bed establishment. 

AMEC did not observe the presence of seagrasses or other SAV, oysters, sponges or associated 

species within the Bridge Assessment Area. During the October 7, 2013 survey, AMEC scientists 

noted the presence of several dolphins swimming in and around the Bridge Assessment Area. 

Loxahatchee River 

Wetland resources within the Bridge Assessment Area at the Loxahatchee River have been 

substantially reduced and limited to fringe wetlands along the shoreline. In areas of the shoreline 

that were not armored during the construction of the existing rail and road bridges, the railroad has 

since placed ballast down to the water’s edge. During the October 7 and 8, 2013 survey, AMEC 

scientists did identify both red mangroves (Rhizophora mangle) and white mangroves growing near 

the existing railroad bridge and approach within the Bridge Assessment Area. Although mangroves 

were noted as being present, Brazilian Pepper and seaside mahoe (Thespesia populnea) were 

noted as being the dominant species within the wetland areas. Both Brazillian pepper and seaside 
Addendum 2 to AAF NOAA Biological Assessment dated September 3, 2013 

AMEC Project No.: 6063120212 January 2014 

Page 6 of 9 

mahoe are FLEPPC listed species. Although seagrass are commonly observed growing throughout 

the central embayment of the Loxahatchee River, seagrasses were not observed within the Bridge 

Assessment Area. AMEC scientists noted that visibility within the river was excellent and the river 

bottom was viewed without obstruction. The bottom of the Bridge Assessment Area was comprised 

mainly of a thin layer of sand and crushed shells. It is assumed that the lack of seagrasses within 

the Bridge Assessment Area is due to the presence of two large bridges that have substantially 

reduced the amount of available light as well as increased the velocity of water moving through the 

Bridge Assessment Area. AMEC did not observe the presence of seagrasses or other SAV, 

oysters, sponges or associated species within the Bridge Assessment Area. During the October 8, 

2013 in-water survey, AMEC scientist identified French angel fish, barracudas, sergeant majors, 

school master snappers, dog faced puffers, as well as various species of grunts swimming around 

the bridges. 

Table 1. In-Stream Habitat at Bridge Crossings 

Name and Mile Post (MP) 

Fresh Water During Site Visit Mangroves Present Red Mangroves Present Seagrasses Observed In-Water Seagrass Survey Performed Johnson's Seagrasses Observed Oyster Beds Observed On Natural Substrate Bottom Substrate 

Eau Gallie (190.47) No Yes No No Yes No No mud, small rocks, 

and crushed shells 

Crane Creek (194.34) Yes No No No Yes No No 

small rocks, 

crushed shells, and 

muck 

Turkey Creek (197.70) Yes No No No Yes* No No muck 

Sebastian River (212.07) No Yes** No No Yes No Yes small rocks, muck, 

and shells 

St. Lucie River (260.93) No Yes Yes No Yes No No small rocks and 

muck 

Loxahatchee River (282.58) No Yes Yes No Yes No No sand and crushed 

shells 

*Benthic survey was limited due to presence of Alligator 

** Mangrove not within project area 
Addendum 2 to AAF NOAA Biological Assessment dated September 3, 2013 

AMEC Project No.: 6063120212 January 2014 

Page 7 of 9 

Table 2. Summary of estimated wetland/surface water impacts at the six Bridge Assessment Areas 

surveyed along the North-South Corridor 

County Name and Mile Post (MP) 

Estimated Direct Impact Area (acres) 

Wetlands Surface Waters 

Brevard 

Eau Gallie (MP 190.47) 0.069 0.212 

Crane Creek (MP 194.34) 0.080 0.347 

Turkey Creek (MP 197.70) 0.003 0.088 

Sebastian River (MP 212.07) 0.046 0.812 

Martin St Lucie River (MP 260.93) 0.008* 0.323* 

Palm Beach Loxahatchee River (MP 282.58) 0.000* 0.317* 

Total Impacts 0.205 2.099

*Currently, no in-water work is proposed at these sites; however, the number listed is the footprint of the bridge 

1.3 Protected Species and Critical Habitat Likely to be Present in the Project Area 

As discussed in the BA, five species of federally listed sea turtles [loggerhead sea turtle (Caretta 

caretta), green sea turtle (Chelonia mydas), Kemp’s ridley sea turtle (Lepidochelys kempii), hawksbill 

sea turtle (Eretmochelys imbricate) and leatherback sea turtle (Dermochelys coriacea)], smalltooth 

sawfish (Pristis pectinata), and Johnson’s seagrass (Halophilia johnsonii) are the federally protected 

species (under NOAA Fisheries jurisdiction) that have the potential to occur within the Project Area. 

2.0 Effects Analysis 

The Bridge Assessment Areas are located along the existing FEC rail corridor and are therefore 

currently impacted by existing freight train traffic. Primary issues associated with this Project for 

protected species under NOAA Fisheries jurisdiction include potential effects from construction 

associated with removal and replacement of bridges. Impact to habitat associated with construction 

include placement of pilings, placement of riprap/fill at the location of abutments, removal of existing 

timber pilings, and shading resulting from bridge construction. Long-term impacts to protected 

species associated with the Project may also include potential disturbance by an increase in noise 

from increased train traffic. To aid in the effect analysis AMEC utilized the Checklist of Information 

Needed to Complete Section 7 Consultation provided by NOAA Fisheries. A checklist for each of the 

six Bridge Assessment Areas is included in Attachment 4. 

Impacts associated with the rehabilitation of the rail bridges within the six Bridge Assessment Areas 

are similar to the impacts outlined in the BA (See Section 4.0). Below is a summary of potential 

impacts to the protected species. 

2.1 Sea Turtle 

The only potential habitat for sea turtles in the Bridge Assessment Areas is located at the Sebastian 

River, St. Lucie River, and Loxahatchee River. It is unlikely sea turtle would be found within the 

other Bridge Assessment Areas. The potential habitat within the Sebastian River, St. Lucie River, 

and Loxahatchee River is limited to a migratory path way, as there is no foraging habitat (SAV) at 

these locations. Based on the findings from the October 2013 benthic surveys, seagrass beds were 

not identified within any of the Bridge Assessment Areas. With strict compliance to the sea turtle 

mitigation measures (described in detail in the BA Section 6.0) and use of air bubble curtains, it is 
Addendum 2 to AAF NOAA Biological Assessment dated September 3, 2013 

AMEC Project No.: 6063120212 January 2014 

Page 8 of 9 

anticipated that the proposed action may affect, but is not likely to adversely affect the protected 

sea turtle species. 

2.2 Smalltooth Sawfish 

The proposed action at the six Bridge Assessment Areas will not result in permanent or temporary 

impacts to mangrove wetlands. Mangroves observed at the Eau Gallie River, the Sebastian River, 

the St. Lucie River, and Loxahatchee River are not anticipated to be effected by the Bridge 

Alternative. Furthermore, it is anticipated that the proposed maintenance activities at the 

Loxahatchee and St. Lucie River bridges will result in no permanent wetland impacts. Mitigation 

measures to reduce potential impacts to smalltooth sawfish will include strict adherence to sea turtle 

and smalltooth sawfish construction conditions (described in detail in the BA Section 6.0). The 

placement of fill and riprap in wetlands resulting from bridge construction are considered permanent 

impacts to jurisdictional wetlands. As a result, an appropriate CWA Section 404 permit will be 

obtained from the USACE prior to construction, and mitigation would be implemented as required by 

wetland permit conditions. With strict adherence to the sea turtle and smalltooth sawfish construction 

conditions and proposed mitigation, it is anticipated that the proposed action may affect, but is not 

likely to adversely affect smalltooth sawfish. 

2.3 Johnson’s Seagrass 

Based on the results of the October 2013 field assessments (summarized in Table 1) it was 

determined that none of the Bridge Assessment Areas have populations of Johnson’s seagrass. 

The water quality protection measures that will be observed at all of the in-water construction areas 

to protect sea turtles and smalltooth sawfish should provide protection to downstream populations of 

seagrasses and other SAV. 

It is anticipated that the proposed action will have no effect to Johnson’s seagrass. 

3.0 Take Analysis 

No direct take is anticipated for federally listed species under NOAA Fisheries jurisdiction. 

4.0 Conservation and Mitigation Measures 

The corridor of the Project passes through important fish and wildlife habitat. Although no direct take 

is anticipated, the measures outlined in the BA will be implemented to reduce or eliminate potential 

environmental impacts associated with the proposed action, including implementation of the Sea 

Turtle and Smalltooth Sawfish Construction Conditions5. 

The placement of fill and riprap in wetlands resulting from bridge construction are considered 

permanent impacts to jurisdictional wetlands. As a result, an appropriate CWA Section 404 permit 

will be obtained from the USACE prior to construction, and mitigation would be implemented as 

required by wetland permit conditions. AAF proposes to purchase credits at approved mitigation 

 

5

 National Marine Fisheries Service (NMFS). 2006. Sea Turtle and Smalltooth Sawfish Construction Conditions. 

http://www.dep.state.fl.us/Water/ wetlands/forms/spgp/SPGP_IV_Attachment_14-Sawfish_SeaTurtlesConstCond.pdf. Accessed 

December 29, 2009. 

[Type text]

Attachment 1

Figures 
Addendum 2 to AAF NOAA Fisheries Biological Assessment dated September 3, 2013

AMEC Project No.: 6063120212 November 2013

Page 1 
[Type text]

Attachment 2

Photograph Log
Addendum 2 to AAF NOAA Fisheries Biological Assessment dated September 3, 2013

AMEC Project No.: 6063120212 November 2013

Page 1 

Photograph 1. Eau Gallie River (Mile Post: 190.47), 

Facing south across the Eau Gallie River

Photograph 2. Eau Gallie River (Mile Post: 190.47), 

White mangrove and saw palmetto growing beneath the bridge
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Photograph 3. Crane Creek Bridge (Mile Post: 194.47), 

Facing south from the northern bank

Photograph 4. Crane Creek Bridge (Mile Post: 194.47), 

Facing north toward to the waterside park

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AMEC Project No.: 6063120212 November 2013

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Photograph 7. Sebastian River (Mile Post: 212.07), Sebastian River FEC Railroad Bridge

Photograph 8. Sebastian River (Mile Post: 212.07), South Side of the Sebastian River 

Railroad Bridge
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AMEC Project No.: 6063120212 November 2013

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Photograph 9. Sebastian River (Mile Post: 212.07), In-water benthic survey

Photograph 10. St. Lucie River Bridge (Mile Post 260.93),

Facing north across the St. Lucie River
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AMEC Project No.: 6063120212 November 2013

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Photograph 11. St. Lucie River Bridge (Mile Post 260.93), Disturbed mangrove wetland 

located on the northern bank of the river

Photograph 12. St. Lucie River Bridge (Mile Post 260.93), Turbid condition of the water 

throughout the St. Lucie River
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AMEC Project No.: 6063120212 November 2013

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Photograph 13. Loxahatchee River Bridge (Mile Post 282.58),

Facing north across the Loxahatchee River

Photograph 14. Loxahatchee River Bridge (Mile Post 282.58),

Example of the sandy covered benthos within the project area
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AMEC Project No.: 6063120212 November 2013

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Photograph 15. Loxahatchee River Bridge (Mile Post 282.58),

Sandy bottom with algae covered shells and rocks

Photograph 16. Loxahatchee River Bridge (Mile Post 282.58), Puffer fish and sergeant 

majors schooling near the algae cover rip rap near the southern shoreline.
Attachment 3

Aerial Photographs
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Attachment 4

ESA Checklists


•For docks, what type of decking will be used? If grated, provide manufacturer's name/

address/grating type, and percent light transmittance (%LT) of the grating design used? 

If wooden planks, what is the proposed spacing between the deckboards (1⁄2-inch, 3⁄4-inch, 

1-inch, other?). Has the applicant been advised that COE-NMFS project review is 

significantly simplified and expedited for dock designs incorporating >43% LT grated 

decking, or 1-inch deckboard- and walkway-spacing, over Johnson's seagrass areas? 

Proposed height of dock? Orientation of the dock (N, S, etc.)?

•Piling construction methodology. Are pile driving methods adequately described and are 

potential impacts to species adequately addressed? Will submerged aquatic vegetation 

(SAV) be impacted by pile installation? If necessary, will the applicant's contractor 

adjust the spacing between piles to avoid driving piles onto Johnson's seagrass? Avoiding 

all piling impacts to JSG will significantly simplify and expedite the COE-NMFS project 

review process.

•Number of new slips and size of slips, if applicable. If new construction includes Highand-Dry boat storage, what is the High-and-Dry vessel storage capacity?

•How big are the boats that are planned to be moored at the dock (either in the water or on a 

boatlift), if known? 

•For all projects not involving docks or marinas (i.e., seawalls, jetties, etc.), please provide 

project description.

•Dredging? If yes, describe depth of cut, dredge type used, how many cubic yards, and 

what will be done with the spoil. Describe bottom sediments. Describe area 

hydrodynamics, i.e., average current speed and direction.

N/A

N/A

N/A

N/A

N/A

Piles will be driven to load bearing capacity for E80 live loads. Piles will be driven with a steel pile 

driving template placed to prevent movement of the pile group. SAV were not observed within the 

project footprint.
•Blasting? If yes, describe explosive weights, blasting plan, etc.

•What is the intended construction schedule (how many days, weeks, or months for inwater work)?

Potential Effects on Species/Critical Habitat:

•Please explain any impacts/effects to the critical habitat's primary constituent elements -

PCEs)? Please identify which critical habitat unit(s) is being affected (e.g., Gulf sturgeon 

have 14 units, seven under NMFS jurisdiction and seven under FWS jurisdiction).

•What will the effects be, if any, to each PCE?

•Square footage to be affected by project?

•Will mangroves be impacted? Explain and quantify impacts.

•How will the habitat be changed/altered as a result of the action? Could or will the 

alteration affect listed species? How?

N/A

N/A

N/A

Work will be completed by December 2016

12,268 sq ft will be affected by the project footprint.

Mangrove impacts and trimming are not anticipated. 

Approximately 12,268 sq. ft. of surface waters and wetlands will be impacted by the installation of 

riprap and pilings, and shading of non-vegetated surface water by the new bridge. The proposed 

bridge construction may have direct short-term adverse effects on the water quality in the project 

vicinity. Effects to the managed species known to occur in the project vicinity would include installation 

of pilings and shade resulting from bridge deck construction. Pilings would ultimately result in a 

beneficial effect to species/life stages that prefer such structures as habitat, such as adult goliath 

grouper, gray snapper, and mutton snapper. Lifecycle functions will not be affected by the proposed

 activities.